OSA's Digital Library

Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 4, Iss. 10 — Oct. 1, 2013
  • pp: 1829–1845

Separating structures of different fluorophore concentrations by principal component analysis on multispectral excitation-resolved fluorescence tomography images

Huangsheng Pu, Wei He, Guanglei Zhang, Bin Zhang, Fei Liu, Yi Zhang, Jianwen Luo, and Jing Bai  »View Author Affiliations

Biomedical Optics Express, Vol. 4, Issue 10, pp. 1829-1845 (2013)

View Full Text Article

Enhanced HTML    Acrobat PDF (1651 KB)

Browse Journals / Lookup Meetings

Browse by Journal and Year


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools



Multispectral excitation-resolved fluorescence tomography (MEFT) uses excitation light of different wavelengths to illuminate the fluorophores and obtains the reconstruction image frame which is fluorescence yield at each corresponding wavelength. For structures containing fluorophores of different concentrations, fluorescence yields show different variation trends with the excitation spectrum. In this study, principal component analysis (PCA) is used to analyze the MEFT reconstructed image frames. By taking advantage of the different variation trends of fluorescence yields, PCA can provide a set of principal components (PCs) in which structures containing different concentrations of fluorophores are shown separately. Simulations and experiments are both performed to test the performance of the proposed algorithm. The results suggest that the location and structure of fluorophores with different concentrations can be obtained and the contrast of fluorophores can be improved further by using this algorithm.

© 2013 OSA

OCIS Codes
(100.3190) Image processing : Inverse problems
(170.3010) Medical optics and biotechnology : Image reconstruction techniques
(170.3660) Medical optics and biotechnology : Light propagation in tissues
(170.3880) Medical optics and biotechnology : Medical and biological imaging
(170.6960) Medical optics and biotechnology : Tomography
(290.1990) Scattering : Diffusion
(290.7050) Scattering : Turbid media

ToC Category:
Image Reconstruction and Inverse Problems

Original Manuscript: June 13, 2013
Revised Manuscript: August 1, 2013
Manuscript Accepted: August 5, 2013
Published: August 29, 2013

Huangsheng Pu, Wei He, Guanglei Zhang, Bin Zhang, Fei Liu, Yi Zhang, Jianwen Luo, and Jing Bai, "Separating structures of different fluorophore concentrations by principal component analysis on multispectral excitation-resolved fluorescence tomography images," Biomed. Opt. Express 4, 1829-1845 (2013)

Sort:  Author  |  Year  |  Journal  |  Reset  


  1. V. Ntziachristos, C. H. Tung, C. Bremer, and R. Weissleder, “Fluorescence molecular tomography resolves protease activity in vivo,” Nat. Med.8(7), 757–761 (2002). [CrossRef] [PubMed]
  2. V. Ntziachristos, E. A. Schellenberger, J. Ripoll, D. Yessayan, E. Graves, A. Bogdanov, L. Josephson, and R. Weissleder, “Visualization of antitumor treatment by means of fluorescence molecular tomography with an annexin V-Cy5.5 conjugate,” Proc. Natl. Acad. Sci. U.S.A.101(33), 12294–12299 (2004). [CrossRef] [PubMed]
  3. X. Montet, V. Ntziachristos, J. Grimm, and R. Weissleder, “Tomographic fluorescence mapping of tumor targets,” Cancer Res.65(14), 6330–6336 (2005). [CrossRef] [PubMed]
  4. A. Corlu, R. Choe, T. Durduran, M. A. Rosen, M. Schweiger, S. R. Arridge, M. D. Schnall, and A. G. Yodh, “Three-dimensional in vivo fluorescence diffuse optical tomography of breast cancer in humans,” Opt. Express15(11), 6696–6716 (2007). [CrossRef] [PubMed]
  5. R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med.9(1), 123–128 (2003). [CrossRef] [PubMed]
  6. X. Michalet, F. F. Pinaud, L. A. Bentolila, J. M. Tsay, S. Doose, J. J. Li, G. Sundaresan, A. M. Wu, S. S. Gambhir, and S. Weiss, “Quantum dots for live cells, in vivo imaging, and diagnostics,” Science307(5709), 538–544 (2005). [CrossRef] [PubMed]
  7. G. Hu, J. Yao, and J. Bai, “Full-angle optical imaging of near-infrared fluorescent probes implanted in small animals,” Prog. Nat. Sci.18(6), 707–711 (2008). [CrossRef]
  8. S. V. Patwardhan, S. R. Bloch, S. A. Achilefu, and J. P. Culver, “Time-dependent whole-body fluorescence tomography of probe bio-distributions in mice,” Opt. Express13(7), 2564–2577 (2005). [CrossRef] [PubMed]
  9. E. E. Graves, J. Ripoll, R. Weissleder, and V. Ntziachristos, “A submillimeter resolution fluorescence molecular imaging system for small animal imaging,” Med. Phys.30(5), 901–911 (2003). [CrossRef] [PubMed]
  10. A. Soubret, J. Ripoll, and V. Ntziachristos, “Accuracy of fluorescent tomography in the presence of heterogeneities: study of the normalized Born ratio,” IEEE Trans. Med. Imaging24(10), 1377–1386 (2005). [CrossRef] [PubMed]
  11. X. Song, D. Wang, N. Chen, J. Bai, and H. Wang, “Reconstruction for free-space fluorescence tomography using a novel hybrid adaptive finite element algorithm,” Opt. Express15(26), 18300–18317 (2007). [CrossRef] [PubMed]
  12. A. Joshi, W. Bangerth, and E. M. Sevick-Muraca, “Adaptive finite element based tomography for fluorescence optical imaging in tissue,” Opt. Express12(22), 5402–5417 (2004). [CrossRef] [PubMed]
  13. A. Ale, R. B. Schulz, A. Sarantopoulos, and V. Ntziachristos, “Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors,” Med. Phys.37(5), 1976–1986 (2010). [CrossRef] [PubMed]
  14. Y. T. Lin, W. C. Barber, J. S. Iwanczyk, W. Roeck, O. Nalcioglu, and G. Gulsen, “Quantitative fluorescence tomography using a combined tri-modality FT/DOT/XCT system,” Opt. Express18(8), 7835–7850 (2010). [CrossRef] [PubMed]
  15. X. Liu, F. Liu, Y. Zhang, and J. Bai, “Unmixing dynamic fluorescence diffuse optical tomography images with independent component analysis,” IEEE Trans. Med. Imaging30(9), 1591–1604 (2011). [CrossRef] [PubMed]
  16. A. D. Klose, “Hyperspectral excitation-resolved fluorescence tomography of quantum dots,” Opt. Lett.34(16), 2477–2479 (2009). [CrossRef] [PubMed]
  17. A. D. Klose and T. Pöschinger, “Excitation-resolved fluorescence tomography with simplified spherical harmonics equations,” Phys. Med. Biol.56(5), 1443–1469 (2011). [CrossRef] [PubMed]
  18. A. J. Chaudhari, S. Ahn, R. Levenson, R. D. Badawi, S. R. Cherry, and R. M. Leahy, “Excitation spectroscopy in multispectral optical fluorescence tomography: methodology, feasibility and computer simulation studies,” Phys. Med. Biol.54(15), 4687–4704 (2009). [CrossRef] [PubMed]
  19. A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol.50(23), 5421–5441 (2005). [CrossRef] [PubMed]
  20. H. Abdi and L. J. Williams, “Principal component analysis,” Wires. Clim. Change.2(4), 433–459 (2010).
  21. N. G. Anderson, A. P. Butler, N. J. Scott, N. J. Cook, J. S. Butzer, N. Schleich, M. Firsching, R. Grasset, N. de Ruiter, M. Campbell, and P. H. Butler, “Spectroscopic (multi-energy) CT distinguishes iodine and barium contrast material in MICE,” Eur. Radiol.20(9), 2126–2134 (2010). [CrossRef] [PubMed]
  22. H. Gao, J. F. Cai, Z. Shen, and H. Zhao, “Robust principal component analysis-based four-dimensional computed tomography,” Phys. Med. Biol.56(11), 3181–3198 (2011). [CrossRef] [PubMed]
  23. P. E. Svensson, J. Olsson, F. Engbrant, E. Bengtsson, and P. Razifar, “Characterization and Reduction of Noise in Dynamic PET Data Using Masked Volumewise Principal Component Analysis,” J. Nucl. Med. Technol.39(1), 27–34 (2011). [CrossRef] [PubMed]
  24. P. Razifar, H. Engler, G. Blomquist, A. Ringheim, S. Estrada, B. Långström, and M. Bergström, “Principal component analysis with pre-normalization improves the signal-to-noise ratio and image quality in positron emission tomography studies of amyloid deposits in Alzheimer’s disease,” Phys. Med. Biol.54(11), 3595–3612 (2009). [CrossRef] [PubMed]
  25. E. Eyal, B. N. Bloch, N. M. Rofsky, E. Furman-Haran, E. M. Genega, R. E. Lenkinski, and H. Degani, “Principal component analysis of dynamic contrast enhanced MRI in human prostate cancer,” Invest. Radiol.45(4), 174–181 (2010). [CrossRef] [PubMed]
  26. E. M. C. Hillman and A. Moore, “All-optical anatomical co-registration for molecular imaging of small animals using dynamic contrast,” Nat. Photonics1(9), 526–530 (2007). [CrossRef] [PubMed]
  27. X. Liu, D. F. Wang, F. Liu, and J. Bai, “Principal component analysis of dynamic fluorescence diffuse optical tomography images,” Opt. Express18(6), 6300–6314 (2010). [CrossRef] [PubMed]
  28. V. Saxena, M. Sadoqi, and J. Shao, “Polymeric nanoparticulate delivery system for Indocyanine green: biodistribution in healthy mice,” Int. J. Pharm.308(1-2), 200–204 (2006). [CrossRef] [PubMed]
  29. M. Choi, K. Choi, S. W. Ryu, J. Lee, and C. Choi, “Dynamic fluorescence imaging for multiparametric measurement of tumor vasculature,” J. Biomed. Opt.16(4), 046008 (2011). [CrossRef] [PubMed]
  30. J. J. Duderstadt and L. J. Hamilton, Nuclear Reactor Analysis(New York:Wiley,1976).
  31. N. M. Anderson and P. Sekelj, “Studies on the determination of dye concentration in nonhemolyzed blood,” J. Lab. Clin. Med.72(4), 705–713 (1968). [PubMed]
  32. R. Simmons and R. J. Shephard, “Does indocyanine green obey Beer’s law?” J. Appl. Physiol.30(4), 502–507 (1971). [PubMed]
  33. M. L. Landsman, G. Kwant, G. A. Mook, and W. G. Zijlstra, “Light-absorbing properties, stability, and spectral stabilization of indocyanine green,” J. Appl. Physiol.40(4), 575–583 (1976). [PubMed]
  34. F. Liu, X. Liu, D. Wang, B. Zhang, and J. Bai, “A parallel excitation based fluorescence molecular tomography system for whole-body simultaneous imaging of small animals,” Ann. Biomed. Eng.38(11), 3440–3448 (2010). [CrossRef] [PubMed]
  35. R. C. Benson and H. A. Kues, “Fluorescence properties of indocyanine green as related to angiography,” Phys. Med. Biol.23(1), 159–163 (1978). [CrossRef] [PubMed]
  36. R. Michels, F. Foschum, and A. Kienle, “Optical properties of fat emulsions,” Opt. Express16(8), 5907–5925 (2008). [CrossRef] [PubMed]
  37. V. Ntziachristos and R. Weissleder, “Charge-coupled-device based scanner for tomography of fluorescent near-infrared probes in turbid media,” Med. Phys.29(5), 803–809 (2002). [CrossRef] [PubMed]
  38. A. Kak and M. Slaney, Computerized Tomographic Imaging (New York: IEEE Press, 1987), ch. 7.
  39. B. Dogdas, D. Stout, A. F. Chatziioannou, and R. M. Leahy, “Digimouse: A 3D whole body mouse atlas from CT and cryosection data,” Phys. Med. Biol.52(3), 577–587 (2007). [CrossRef] [PubMed]
  40. G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol.50(17), 4225–4241 (2005). [CrossRef] [PubMed]
  41. G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Effect of optical property estimation accuracy on tomographic bioluminescence imaging: simulation of a combined optical-PET (OPET) system,” Phys. Med. Biol.51(8), 2045–2053 (2006). [CrossRef] [PubMed]
  42. X. Intes, V. Ntziachristos, J. P. Culver, A. Yodh, and B. Chance, “Projection access order in algebraic reconstruction technique for diffuse optical tomography,” Phys. Med. Biol.47(1), N1–N10 (2002). [CrossRef] [PubMed]
  43. S. R. Arridge, “Optical tomography in medical imaging,” Inverse Probl.15(2), R41–R93 (1999). [CrossRef]
  44. H. Dehghani, M. E. Eames, P. K. Yalavarthy, S. C. Davis, S. Srinivasan, C. M. Carpenter, B. W. Pogue, and K. D. Paulsen, “Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction,” Commun. Numer. Methods Eng.25(6), 711–732 (2009). [CrossRef] [PubMed]

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited